The present invention provides a pixel arrangement method that reduces color shift of pattern retarder glasses based 3D display system and includes: providing a display panel, which includes a substrate and a plurality of primary pixels that is formed on the substrate in an array; dividing the primary pixels in 3D mode displaying in such a way that each of the primary pixels is divided into four sub-pixels, wherein the sub-pixels are of colors that are pure colors and two adjacent ones of the sub-pixels in either horizontal or vertical direction are of different colors; and dividing the primary pixels in 2D mode displaying in such a way that each of the primary pixels is divided into three or four sub-pixels, wherein the sub-pixels are of colors that are pure colors and two adjacent ones of the sub-pixels in either horizontal or vertical direction are of different colors.